rs8109507

chr19-40905329-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000651727.1(CYP2G1P):n.1058-6365C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0541 in 152,184 control chromosomes in the GnomAD database, including 248 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.054 (248 hom., cov: 31)
• Consequence: CYP2G1P ENST00000651727.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110

Genes affected

CYP2G1P (HGNC:2633): (cytochrome P450 family 2 subfamily G member 1, pseudogene) Predicted to enable heme binding activity and monooxygenase activity. Predicted to be involved in epoxygenase P450 pathway and xenobiotic catabolic process. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CYP2G1P	ENST00000651727.1	n.1058-6365C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0541 AC: 8230 AN: 152066 Hom.: 247 Cov.: 31

Gnomad AFR AF: 0.0531

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0159

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0618

Gnomad OTH AF: 0.0699

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0541 AC: 8226 AN: 152184 Hom.: 248 Cov.: 31 AF XY: 0.0507 AC XY: 3774 AN XY: 74406

Gnomad4 AFR AF: 0.0530

Gnomad4 AMR AF: 0.0552

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0441

Gnomad4 FIN AF: 0.0159

Gnomad4 NFE AF: 0.0618

Gnomad4 OTH AF: 0.0687

Alfa AF: 0.0581 Hom.: 129

Bravo AF: 0.0564

Asia WGS AF: 0.0160 AC: 56 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.3
Dann	Benign	0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8109507; hg19: chr19-41411234;